Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment.
Bottom Line: Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation.Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding.These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.
Affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.Show MeSH
Related in: MedlinePlus
Mentions: RNA was isolated from independent preparations of the indicated cell type using the RNeasy mini prep kit (Qiagen) and quantitative real-time RT-PCR (qRT-PCR) performed as previously described (45). Primers used in this study are listed in Supplemental Table S2. 18s rRNA was measured and used to normalize between samples. For each gene, qRT-PCR was performed at the same time for all cell lines examined, creating a single dataset for each gene. These data were then used as indicated in the generation of Figure 4, Table 1 and Supplemental Figure S1. Normalized data from three independent preparations were averaged and plotted as fold over the Raji cell samples. Student's t-tests were used to determine statistical significance between cell types and variation was represented by standard error of the mean (SEM).
Affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.